Ring-Stacking Water Clusters: Morphology and Stabilities

Ice structures assembled from cubic water clusters of D2d and S4 symmetry

The study of self-assembly processes is of key importance for fundamental science and modern technologies. Cubic water clusters of D2d and S4 symmetry show great potential as building blocks for self-assembly. The objective of this paper is to construct possible ice structures formed by hydrogen bonding of these very stable water clusters. A number of such structures are herein presented, including quasi-2D and 3D ices as well as spatial layered and tubular ices. The energetics and structure of many configurations differing in the arrangement of hydrogen atoms in hydrogen bonds have been studied. It was established that the proton disorder of all such ices is of island type. The residual entropy of these ices is equal to ln(3)/4 in dimensionless form. For layered structures formed by the stacking of multiple bilayers, the determining role of the van der Waals interactions is shown. Note that, for all considered ices, the lowest-energy configurations are formed only by clusters of D2d symmetry.

Adsorption free energy of phenol onto coronene: Solvent and temperature effects

Molecular modeling can considerably speed up the discovery of materials with high adsorption capacity for wastewater treatment. Despite considerable efforts in computational studies, the molecular modeling of adsorption processes has several limitations in reproducing experimental conditions. Handling the environmental effects (solvent effects) and the temperature effects are part of the important limitations in the literature. In this work, we address these two limitations using the adsorption of phenol onto coronene as case study. In the proposed model, for the solvent effects, we used a hybrid solvation model, with n explicit water molecules and implicit solvation. We increasingly used n=1 to n=12 explicit water molecules. To account for the temperature effects, we evaluated the adsorption efficiency using the adsorption free energy for temperatures varying from 200 to 400K. We generated initial configurations using classical molecular dynamics, before further optimisation at the ωB97XD/aug-cc-pVDZ level of theory. Polarisable continuum solvation model (PCM) is used for the implicit solvation. The adsorption free energy is evaluated to be -1.3kcal/mol at room temperature. It has been found that the adsorption free energy is more negative at low temperatures. Above 360K, the adsorption free energy is found to be positive.

Water clusters and density fluctuations in liquid water based on extended hierarchical clustering methods

The microscopic structures of liquid water at ambient temperatures remain a hot debate, which relates with structural and density fluctuations in the hydrogen bond network. Here, we use molecular dynamics simulations of liquid water to study the properties of three-dimensional cage-like water clusters, which we investigate using extended graph-based hierarchical clustering methods. The water clusters can cover over 95% of hydrogen bond network, among which some clusters maximally encompass thousands of molecules extending beyond 3.0 nm. The clusters imply fractal behaviors forming percolating networks and the morphologies of small and large clusters show different scaling rules. The local favored clusters and the preferred connections between adjacent clusters correspond to lower energy and conformational entropy depending on cluster topologies. Temperature can destroy large clusters into small ones. We show further that the interior of clusters favors high-density patches. The water molecules in the small clusters, inside which are the void regarded as hydrophobic objects, have a preference for being more tetrahedral. Our results highlight the properties and changes of water clusters as the fundamental building blocks of hydrogen bond networks. In addition, the water clusters can elucidate structural and density fluctuations on different length scales in liquid water.

Hierarchical clustering analysis of hydrogen bond networks in aqueous solutions

To understand the relation between the macroscopic properties and microscopic structure of hydrogen bond networks in solutions, we introduced a hierarchical clustering method to analyze the typical configurations of water clusters in this type of network. Regarding hydrogen bonds as frames, the rings, fragments and clusters are defined and analyzed to provide a comprehensive perspective for the distributional and dynamic characteristics of the hydrogen-bonding network in NaCl solution at different concentrations. The properties of the radial distribution function and hydrogen bonds are first analyzed. Destruction and shorter lifetimes of hydrogen bonds are observed in solutions. In further analysis of the two-dimensional configuration, i.e., ring, and three-dimensional configuration, i.e., fragment, the average number, size and lifetime of these structures consistently decrease as the concentration increases. Ionic effects on disrupting rings and fragments are significant in the first hydration shell, especially with sodium cations, and these effects weaken beyond the first hydration shell. Regarding the clusters obtained using the Louvain algorithm, our results indicate that clusters break and become smaller as the NaCl concentration increases. The presence of ions also leads to the isolation of clusters and therefore the inhibition of changes. The lifetime of clusters increases with NaCl concentration, indicating the slowed breakage and reformation of clusters in NaCl solutions. This method can be further applied to quantitatively characterize hydrogen bond networks to elucidate more properties of aqueous solutions.

Comparative Study of Proton Exchange in Tri- and Hexatitanates: Correlations between Stability and Electronic Properties

A hydrothermal method is considered to be convenient and is extensively used in preparing titanate architectures, but the intermediate and final products are complicated and variable. To date, it is accepted that intermediates are tri- and hexatitanates. Here, atomic structures, energetics, and correlations between stability and electronic properties of proton exchange in tri- and hexatitanates, i.e., Na_2-xH_xTi₃O₇ and Na_2-xH_xTi₆O₁₃, are investigated by first-principles calculations. We found that the bond length of Na-O bonds plays a significant role in determining the activity of tunnel oxygen atoms, while the proton substitution sites are closely related to the activity of tunnel O atom in titanates. As H⁺ concentration increases, the formation energy of Na_2-xH_xTi₃O₇ and Na_2-xH_xTi₆O₁₃ decreases first and then increases, suggesting that completely protonated titanates, i.e., H₂Ti₃O₇ and H₂Ti₆O₁₃, are unstable. However, we found that H⁺ substitution would take place even in an alkaline solution both for Na₂Ti₃O₇ and Na₂Ti₆O₁₃. With a decrease in the pH, the process of H⁺ exchange becomes more energetically favorable. Compared to Na₂Ti₃O₇, Na⁺ ions are more easily exchanged by H⁺ ions in Na₂Ti₆O₁₃ at the same pH value. We found that there is a strong correlation between stability and electronic properties during the Na⁺-H⁺ exchange process. Finally, hydrogen bonds are observed in H₂Ti₃O₇ and Na_2-xH_xTi₆O₁₃ complexes, which make them more stable than Na_2-xH_xTi₃O₇ complexes without H-bonds. All of these findings provide insight into understanding the geometry of possible intermediates in the preparation of titanates and suitable conditions for the synthesis of titanates.

Effect of the co-adsorption of small molecules from air on the properties of penta-graphene and their proton transfer calculation

Penta-graphene has attracted considerable attention due to its unique structure and novel properties. Herein, we studied the effect of the co-adsorption of small molecules from air on the properties of penta-graphene using first-principles calculations. Our results show that oxygen molecules can be self-decomposed on the surface of penta-graphene and the process of O₂ decomposition is an exothermic reaction. On the contrary, the adsorption of H₂O or N₂ molecule on penta-graphene exhibits weak interaction characteristic. For co-adsorption systems, the adsorption of N₂ molecule has no effect on the electronic properties of penta-graphene because the N₂ molecule is more inert than other molecules. Hydrogen bonds (H-bonds) have been observed in the co-adsorption of H₂O and O₂ on penta-graphene. We find that shorter H-bonds lead to higher stability of the systems. We also explore the proton transfer process between H₂O and oxidized penta-graphene. Our results show that the proton transfer process is relatively difficult due to the high energy barrier. However, double-proton transfer is an exothermic process since the energy of the final state is 0.11 eV lower than that of the initial state. These results indicate that the configuration of oxidized penta-graphene is complicated. Our research provides a theoretical basis and important guidance for the experimental synthesis and functionalization of penta-graphene.

A hierarchical clustering method of hydrogen bond networks in liquid water undergoing shear flow

Many properties of water, such as turbulent flow, are closely related to water clusters, whereas how water clusters form and transform in bulk water remains unclear. A hierarchical clustering method is introduced to search out water clusters in hydrogen bonded network based on modified Louvain algorithm of graph community. Hydrogen bonds, rings and fragments are considered as 1st-, 2nd-, and 3rd-level structures, respectively. The distribution, dynamics and structural characteristics of 4th- and 5th-level clusters undergoing non-shear- and shear-driven flow are also analyzed at various temperatures. At low temperatures, nearly 50% of water molecules are included in clusters. Over 60% of clusters remain unchanged between neighboring configurations. Obvious collective translational motion of clusters is observed. The topological difference for clusters is elucidated between the inner layer, which favors 6-membered rings, and the external surface layer, which contains more 5-membered rings. Temperature and shearing can not only accelerate the transformation or destruction of clusters at all levels but also change cluster structures. The assembly of large clusters can be used to discretize continuous liquid water to elucidate the properties of liquid water.

Steric Effect of a Capping Ligand on the Formation of Supramolecular Coordination Networks of Ni(II): Solid-State Entrapment of Cyclic Water Dimer

Supramolecular dimer of water is the simplest of the small water clusters [(H₂O) _n , n = 2-10]. During the course of our work on supramolecular coordination networks of three-component systems (divalent metal ion, tridentate capping ligand, and ditopic carboxylate linker), a cyclic water dimer is found to be entrapped in the network of [Ni₂(6-Mebpta)₂(adc)₂]·2H₂O (1) (6-Mebpta = 2-methyl-N-((6-methylpyridin-2-yl)methyl)-N-(pyridin-2-ylmethyl)propan-2-amine and adc = acetylenedicarboxylate). Based on the single-crystal structure of 1, the water dimer plays an important role in connecting the bis(adc) bridged dinickel synthons to form a one-dimensional (1D) supramolecular network. To emphasize the role of 6-Mebpta in the judicious choice of components for 1, one simple modification to it by having another methyl group in the second pendant pyridyl group to make 6,6'-Me₂bpta (2-methyl-N,N-bis((6-methylpyridin-2-yl)methyl)propan-2-amine) did not allow the formation of any water cluster in [Ni(6,6'-Me₂bpta)(adc)(H₂O)]·H₂O (2), where a different coordination environment around Ni(II) is also observed. Further quantification of the difference in supramolecular interactions observed in 1 and 2 has been assessed by Hirshfeld surface analysis. Both 1 and 2 are obtained in good yields at room temperature (methanol as solvent) and are further characterized by elemental analysis, Fourier transform infrared (FTIR) and Raman spectroscopy, powder X-ray diffraction, and thermogravimetric analysis.

Ring-Stacking Water Clusters: Morphology and Stabilities

The structures and interaction energies of water clusters with ring stacking motifs are studied by using ab initio calculations. The structures of the water clusters are constructed by stacking either single rings or multi-rings of tetramer, pentamer, and hexamer. We found that, in the single-ring-stacking motif, the most stable isomers exhibit an alternative clockwise-anticlockwise stacking pattern. We also show that four-layer single-ring-stacking isomers are not energetically favorable in comparison with those of two-layer multi-ring-stacking isomers. The relative stability of the isomers is also analyzed in terms of H-bond strength and elastic distortions of the water molecules.